# Description: Sequence Alignment/Map Tools version 0.1.19
# URL: http://samtools.sourceforge.net/
# Maintainer: Petar Petrov, slackalaxy at gmail dot com
# Depends on:

name=samtools0
version=0.1.19
release=1
source=(http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2)

build() {
	cd samtools-$version
	
	# Use our CFLAGS/CXXFLAGS
	sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile

	make
	make razip

	# Install samtools, razip and bam library
	install -D -m755 samtools $PKG/usr/bin/samtools0
	install -D -m755 razip	  $PKG/usr/bin/razip0
	install -D -m644 libbam.a $PKG/usr/lib/libbam.a

	# Install bcftools its library and vsfutils
	cd bcftools
	install -D -m755 bcftools $PKG/usr/bin/bcftools0
	install -D -m644 libbcf.a $PKG/usr/lib/libbcf.a
	install -D -m755 vcfutils.pl $PKG/usr/bin/vcfutils0.pl

	# Include additional executables
	cd ../misc
	install -D -m755 ace2sam	$PKG/usr/lib/$name/ace2sam
	install -D -m755 bamcheck	$PKG/usr/lib/$name/bamcheck
	install -D -m755 maq2sam-long	$PKG/usr/lib/$name/maq2sam-long
	install -D -m755 maq2sam-short	$PKG/usr/lib/$name/maq2sam-short
	install -D -m755 md5fa		$PKG/usr/lib/$name/md5fa
	install -D -m755 md5sum-lite	$PKG/usr/lib/$name/md5sum-lite
	install -D -m755 wgsim		$PKG/usr/lib/$name/wgsim

	# Include some scripts
	mkdir -p $PKG/usr/share/$name
	cp -a *.pl *.lua *.py plot-bamcheck \
	$PKG/usr/share/$name

	# Include bam header files
	cd ..
	mkdir -p  $PKG/usr/include/bam
	for f in *.h ; do
	  install -m644 $f "$PKG/usr/include/bam"
	done
}